Table of Contents - ms-sequest-0.2.1 Documentation
Pages
Classes and Modules
- MS
- MS::Ident
- MS::Ident::Pepxml
- MS::Ident::Pepxml::SearchHit
- MS::Sequest
- MS::Sequest::Params
- MS::Sequest::Pepxml
- MS::Sequest::Pepxml::Modifications
- MS::Sequest::Sqt
- MS::Sequest::Sqt::Header
- MS::Sequest::Sqt::Locus
- MS::Sequest::Sqt::Match
- MS::Sequest::Sqt::Match::Percolator
- MS::Sequest::Sqt::Spectrum
- MS::Sequest::SqtGroup
- MS::Sequest::Srf
- MS::Sequest::Srf::Dta
- MS::Sequest::Srf::DtaGen
- MS::Sequest::Srf::Header
- MS::Sequest::Srf::NoSequestParamsError
- MS::Sequest::Srf::Out
- MS::Sequest::Srf::Out::Peptide
- MS::Sequest::Srf::Out::Protein
- MS::Sequest::Srf::Pepxml
- MS::Sequest::Srf::Search
- MS::Sequest::Srf::Sqt
Methods
- ::commandline — MS::Sequest::Srf::Pepxml
- ::commandline — MS::Sequest::Srf::Search
- ::commandline — MS::Sequest::Srf::Sqt
- ::db_info — MS::Sequest::Sqt
- ::db_md5sum — MS::Sequest::Sqt
- ::db_seq_length_and_locus_count — MS::Sequest::Sqt
- ::from_io — MS::Sequest::Srf::Header
- ::from_io — MS::Sequest::Srf::DtaGen
- ::from_io — MS::Sequest::Srf::Dta
- ::from_io — MS::Sequest::Srf::Out
- ::from_io — MS::Sequest::Srf::Out::Peptide
- ::from_line — MS::Sequest::Sqt::Locus
- ::get_sequest_params_and_finish_pos — MS::Sequest::Srf
- ::new — MS::Sequest::Params
- ::new — MS::Sequest::Pepxml::Modifications
- ::new — MS::Sequest::SqtGroup
- ::new — MS::Sequest::Sqt
- ::new — MS::Sequest::Sqt::Locus
- ::new — MS::Sequest::Srf
- ::read_extra_references — MS::Sequest::Srf::Out::Peptide
- ::set_deltacn — MS::Sequest::Sqt::Spectrum
- ::set_deltacn_from_deltacn_orig — MS::Sequest::Srf::Out::Peptide
- ::spectra_from_handle — MS::Sequest::Sqt::Spectrum
- ::update_deltacns_from_xcorr — MS::Sequest::Srf::Out::Peptide
- #_sys_ind_basename — MS::Sequest::Params
- #create_static_mods — MS::Sequest::Pepxml::Modifications
- #database — MS::Sequest::Params
- #database_path= — MS::Sequest::Params
- #dta_start_byte — MS::Sequest::Srf
- #enzyme — MS::Sequest::Params
- #enzyme_specificity — MS::Sequest::Params
- #extension — MS::Sequest::SqtGroup
- #filter_by_precursor_mass_tolerance! — MS::Sequest::Srf
- #first_entry — MS::Sequest::Sqt::Locus
- #first_entry — MS::Sequest::Srf::Out::Protein
- #fragment_ion_tol — MS::Sequest::Params
- #fragment_mass_type — MS::Sequest::Params
- #from_file — MS::Sequest::Sqt
- #from_file — MS::Sequest::Srf
- #from_handle — MS::Sequest::Sqt::Header
- #from_io — MS::Sequest::Srf::Header
- #from_io — MS::Sequest::Srf::DtaGen
- #from_line — MS::Sequest::Sqt::Spectrum
- #from_line — MS::Sequest::Sqt::Match
- #from_lines — MS::Sequest::Sqt::Header
- #get_null_padded_string — MS::Sequest::Srf::Header
- #grab_params — MS::Sequest::Params
- #id — MS::Sequest::Sqt::Locus
- #inspect — MS::Sequest::Srf::Dta
- #inspect — MS::Sequest::Srf::Out
- #inspect — MS::Sequest::Srf::Out::Peptide
- #mass_index — MS::Sequest::Params
- #max_num_differential_AA_per_mod — MS::Sequest::Params
- #max_num_internal_cleavages — MS::Sequest::Params
- #method_missing — MS::Sequest::Params
- #min_number_termini — MS::Sequest::Params
- #modification_info — MS::Sequest::Pepxml::Modifications
- #modifications — MS::Sequest::Pepxml::Modifications
- #negative_q_value — MS::Sequest::Sqt::Match::Percolator
- #negative_q_value= — MS::Sequest::Sqt::Match::Percolator
- #num_dta_files — MS::Sequest::Srf::Header
- #parse_file — MS::Sequest::Params
- #parse_io — MS::Sequest::Params
- #peptide_mass_tol — MS::Sequest::Params
- #percolator_score — MS::Sequest::Sqt::Match::Percolator
- #percolator_score= — MS::Sequest::Sqt::Match::Percolator
- #precursor_mass_type — MS::Sequest::Params
- #probability — MS::Sequest::Sqt::Match::Percolator
- #protein_class — MS::Sequest::Sqt
- #protein_class — MS::Sequest::Srf
- #proteins — MS::Sequest::Sqt::Match
- #q_value — MS::Sequest::Sqt::Match::Percolator
- #read_dta_and_out_interleaved — MS::Sequest::Srf
- #read_dta_files — MS::Sequest::Srf
- #read_out_files — MS::Sequest::Srf
- #read_scan_index — MS::Sequest::Srf
- #reference — MS::Sequest::Sqt::Locus
- #round — MS::Sequest::Srf::Dta
- #sample_enzyme — MS::Sequest::Params
- #sample_enzyme_hash — MS::Sequest::Params
- #search_class — MS::Sequest::SqtGroup
- #sequence — MS::Sequest::Params
- #set_hashes — MS::Sequest::Pepxml::Modifications
- #set_modifications — MS::Sequest::Pepxml::Modifications
- #static_mods — MS::Sequest::Params
- #to_dta — MS::Sequest::Srf::Search
- #to_dta_file_data — MS::Sequest::Srf::Dta
- #to_mgf — MS::Sequest::Srf::Search
- #to_pepxml — MS::Sequest::Srf::Pepxml
- #to_sqt — MS::Sequest::Srf::Sqt
- #version — MS::Sequest::Params
- #write_dta_file — MS::Sequest::Srf::Dta